1999/10/01 by Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky +4 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Fractal and DNA sequence analysis #Machine Learning in Bioinformatics #Genomics and Phylogenetic Studies
paper · doi:10.1089/106652799318364
openalex publication_date 1999/10/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/11
This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.